Cation exchanged clinoptilolite has emerged as an adsorbent that may be used for the treatment of natural gas type mixtures containing excess amounts of nitrogen. In this study, natural clinoptilolite was modified through Fe3+ and Cs+ cation exchange. The resultant mineral phase and elemental composition were verified and the extra framework cation type, charge, and distribution is shown to have a profound effect on the observed adsorptive properties. Single gas adsorption isotherms were conducted at 15 °C and/or 30 °C for CH4 and N2 using a microgravimetric adsorption analyser, and the ideal equimolar CH4/N2 selectivity values were determined for the natural and modified clinoptilolites. Natural clinoptilolite presents selectivity values close to 1. However, we demonstrate that clinoptilolite cation-exchanged with Cs+ and Fe3+ cations is rendered preferentially adsorptive for CH4 over N2 with a higher CH4/N2 selectivity than many adsorbents reported in the literature. The experimental CH4–N2 binary adsorption behavior was evaluated for the first time on raw clinoptilolite and was compared to the modified clinoptilolites with Cs+ and Fe3+ exchanged cations using the concentration pulse chromatographic technique. The experimental binary isotherms showed non-ideal behavior with competitive adsorption between CH4 and N2. In most cases, the theoretical models could not adequately describe the experimental adsorption behavior. Within the temperature range studied of 15 °C and 30 °C, the binary CH4/N2 separation factors range from 2.7 to 5.3, and 3.9 to 7.3 for Cs+ and Fe3+ exchanged clinoptilolite, respectively. These results are comparable or better than those found in literature for activated carbon which typically ranges from 2.1 to 5.5 and may serve as an alternative adsorbent for this type of separation which warrants further investigation.